Shawnee, Kansas-based E3 filed a breach of contract complaint against Biothane Corp., Dilling Mechanical Contractors Inc. and Perennial Energy Inc. on Tuesday in the U.S. District Court for the District of Nebraska.

The three companies worked on a troubled ethanol plant — finished but since mothballed — that an E3 predecessor commissioned near Mead, Neb. Biothane supplied a $1.5...